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In my experience it is best to use a different process to upgrade Puppet than Puppet. The problem is that updating the package can cause the daemon to exit. Updating facter can break the running Puppet daemon as well.

The process I use involves using mcollective to stop the daemon, then install the new facter, puppet, or puppet-common depending on the distro. Once the packages are in place start the daemon. The method doesn't really matter as long as it's outside of the Puppet agent run.

Bonus problem: Puppet agent restarts the Puppet master its connecting to and then can't get the rest of the files to complete the catalog run.